Correction of diffusion calculations when using two types of non- rectangular simulation boxes in molecular simulations

T Cao and XF Ji and JP Wu and SJ Zhang and XF Yang, JOURNAL OF MOLECULAR MODELING, 25, 22 (2019).

DOI: 10.1007/s00894-018-3910-6

Although simulation boxes used in molecular dynamics are normally chosen to be cubic or rectangular, two other cell shapes that are very familiar to crystallographersthe truncated octahedron and the rhombic dodecahedroncould also be used because they are also space-filling cells. Due to their spherical nature, these boxes have been intentionally applied in simulations of biomolecular solutions and liquid structures. Indeed, due to the advantages of running many molecular dynamic codes in parallel, simulations based on these non- rectangular boxes have been growing in popularity in recent years. In this work, the effects of using these two types of boxes on diffusion are explored for the first time, and an appropriate correction formula is derived theoretically within the framework of hydrodynamics. In addition, the range of validity for the correction formula is evaluated by performing molecular dynamic simulations on argon at three different densities.

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